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NEWS.md

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einprot 0.9.5

  • Add filtering by score and number of peptides to Spectronaut workflow
  • Filter by modifications after the normalization in PD-TMT peptide groups workflow

einprot 0.9.4

  • Add details about DIA-NN command line to report
  • Add column with links to ComplexPortal query to link table
  • Include pathways from MSigDB among supported feature collections
  • Update DIA-NN example data
  • Expand input data paths in run*Analysis() functions
  • Add support for importing Spectronaut PG pivot files
  • Add initial support for reading Spectronaut setup.txt files
  • Add BioGRID column in link table
  • Add summary statistic for the number of detected features

einprot 0.9.3

  • Significantly expand the built-in complex database by adding complexes from the Complex Portal and hu.MAP 2.0
  • Hide box plot legends if there are too many groups
  • Add MinProbGlobal imputation method
  • Add makeInteractiveVolcano argument to plotVolcano

einprot 0.9.2

  • Fix sample column name in DIA-NN import
  • Adapt DIA-NN log import to handle vector output
  • Add argument addHeatmaps to run functions, to allow suppression of heatmaps for large data sets
  • Remove samples with no detected features
  • Add support for Spectronaut protein group output
  • Add support for displayName column in sample annotation table
  • Add extraFeatureCols argument for specification of user-defined feature annotation columns
  • Extract information about Top N ions for FragPipe

einprot 0.9.1

  • Replace ggseqlogo dependency with motifStack
  • Adapt missing value plots to work with both proportions and percentages

einprot 0.9.0

  • Consolidate tool-specific templates into a single template

einprot 0.8.0

  • Add support for DIA-NN protein group data

einprot 0.7.7

  • Change default value of singleFit to TRUE everywhere, for consistency

einprot 0.7.6

  • Bug fix in filtering plot when only one criterion is available

einprot 0.7.5

  • Move QC plot function

einprot 0.7.4

  • Add argument to allow limiting the labeling to only features with positive/negative logFCs
  • Add function to generate heatmaps
  • Add function to create summary of abundance values for significant features
  • Add argument to define the assays(s) to use for exported values and barplots
  • Harmonize treatment of merged groups in runTest and plotVolcano
  • Sort exported test results by p-value instead of logFC
  • Expand the set of allowed species

einprot 0.7.3

  • Combine download buttons and pagelength selection for tables
  • Add check and stop if no features are left after filtering

einprot 0.7.2

  • Add option to export link table to csv
  • Add summary table with sequence windows to PTM workflow
  • Add shiny app to generate sequence logos for PTMs
  • Add link to workflow overview in table of contents
  • Include link to top feature sets for each comparison in table of contents

einprot 0.7.1

  • Add scale and subset_row arguments to doPCA
  • Move definition of feature IDs after the filtering
  • Extract FragPipe decoy pattern from the config file
  • Remove features with too few non-imputed values before doing PCA
  • Retain a few more rowData columns for MaxQuant
  • Fix extraction of fixed modifications for MQ v2.2
  • Add max peptide mass and min peptide length to MQ report
  • Add Top3 to the valid iColPatterns
  • Include Top3 abundances in MQ result tables if available

einprot 0.7.0

  • Change approach for injecting values into the Rmd file, to avoid the need to duplicate escapes
  • Allow the user to set the column to colour by in the PCA
  • Include 'extra' columns in output from runPTMTest
  • Allow '^Abundance.' iColPattern
  • Suggest closest iColPattern if the provided one is invalid

einprot 0.6.10

  • Adapt readFragPipeInfo to handle different FragPipe versions
  • Add filtering function for FragPipe
  • Add option to use sample weights for limma
  • Move modifications filters from the PDTMTptm to the PDTMT PeptideGroups workflow
  • Add interactiveGroupColumn argument

einprot 0.6.9

  • Safeguard against non-functional connection to STRING server
  • Allow disabling score/number of peptides/PTMs filters
  • Don't fail if interactiveDisplayColumns are not present in data
  • Use Perl-compatible regular expressions when matching link table columns
  • Include Sequence column in final SCE for PD-TMT data

einprot 0.6.8

  • Add idCol and labelCol arguments to PTM workflow
  • Change default behaviour of fixFeatureIds when column name is given to not make output unique
  • Add stringVersion and stringDir arguments, allowing the use of local STRING files
  • Make filter functions more robust to missing columns
  • Add possibility to write excluded features to a file
  • Represent link table columns as integers/factors when appropriate
  • Allow displaying any column in rowData(sce) in the interactive volcano plot tooltip
  • In the case of long labels, attempt to auto-adapt text size in PCA coefficient and logFC plots
  • Add overview and crosslinks in the beginning of the reports
  • Include bar plot of significant features in pdf output
  • Allow iColPattern without Sample for PDTMT
  • Make plot axis labels less ambiguous

einprot 0.6.7

  • Add signifDigits argument to makeDbLinkTable, and round to 4 significant digits in the templates
  • Include the maximum number of missed cleavages in PDTMT tables
  • Let maxNbrComplexesToPlot determine also the maximum number of top feature sets displayed in the reports
  • Bugfix for sample plot ordering in complex bar plots
  • Add bar plot for significant features

einprot 0.6.6

  • Bring FragPipe workflows up to date
  • Add individual PTM volcano plots to table of content
  • Add modificationsCol and keepModifications arguments to PTM workflow
  • Increase control level in deparsing to allow e.g. multi-line functions
  • Fill feature sets plot by direction
  • Suppress legend in PCA plot if there are too many groups
  • Add option to only retain master proteins in PDTMT Proteins workflow
  • Allow inclusion of extra columns in the link table

einprot 0.6.5

  • Change correlation heatmap appearance
  • Provide the possibility to run the workflows without statistical tests
  • Allow specifying the iColPattern without escaped periods
  • Add interactiveDisplayColumns arguments to volcano plots

einprot 0.6.4

  • Include test results and comparison list in returned SummarizedExperiment
  • Expand the PCA plots with scree plots and coefficient plots
  • Add option to label any/only significant features in volcano plot
  • Add einprotLabel column to link table

einprot 0.6.3

  • Combine PTM tests into a single function

einprot 0.6.2

  • Lift out PTM tests into separate functions
  • Change interface to defining protein ID column in PTM workflow
  • Add tour to iSEE script

einprot 0.6.1

  • Use only spike features with no missing values for normalization
  • Add stringIdCol argument
  • Lift out filtering and SA plots into separate functions

einprot 0.6.0

  • Change handling of feature identifiers - new arguments idCol, labelCol

einprot 0.5.22

  • Check STRING connection, skip STRING analysis in case of problems

einprot 0.5.21

  • Add idCol argument to PD-TMT workflow

einprot 0.5.20

  • Add samSignificance argument to runTest

einprot 0.5.19

  • Bugfix in PTM workflow to correctly access comparisons
  • Add function to map UniProtIDs to gene symbols
  • Include STRING networks also for PD-TMT workflow
  • Allow t-test for PD-TMT workflow

einprot 0.5.18

  • Allow also Abundances.grouped for PD data

einprot 0.5.17

  • Allow custom names of comparisons

einprot 0.5.16

  • Show only features that are significant in at least one comparison in upset plot
  • Expand capabilities of test (a group can belong to more than one merged group, a group can be tested against its complement)

einprot 0.5.15

  • Move normalization to a separate function
  • Allow estimating normalization factors from spike features
  • Move normalization before imputation

einprot 0.5.14

  • Use eBayes rather than treat if minlFC = 0
  • Allow using proDA for differential abundance testing
  • Allow the user to specify which PD quantification file to use
  • Allow running PD workflow without pdAnalysis file
  • Add first version of PD-TMT PTM workflow

einprot 0.5.13

  • Update readFragPipeInfo to use log file instead of config file

einprot 0.5.12

  • Swap UpsetR for ComplexUpset for simplicity
  • Include individual volcano plots in table of contents

einprot 0.5.11

  • Update link to download CORUM complexes

einprot 0.5.10

  • Reset paths
  • Switch to ComplexUpset for filtering plot
  • Use PMID for custom complexes if available

einprot 0.5.9

  • Add decoy filtering for FragPipe output

einprot 0.5.8

  • Don't do upset plots with only one non-empty set

einprot 0.5.7

  • Add FragPipe analysis workflow

einprot 0.5.6

  • Allow subtraction of background as a means of batch correction

einprot 0.5.5

  • Expand description of EMM plots
  • Move references to bib file

einprot 0.5.4

  • Add support for reading FragPipe quantifications

einprot 0.5.3

  • Allow specifying the columns to use as primary/secondary feature IDs

einprot 0.5.2

  • Allow running MQ workflow without XML file

einprot 0.5.1

  • Bugfix for features with p-value = 0 in the volcano plots

einprot 0.5.0

  • Switch to a more modular implementation

einprot 0.4.6

  • Allow providing a sample annotation table in TMT workflow

einprot 0.4.5

  • Allow providing a sample annotation table in MQ workflow

einprot 0.4.4

  • Display (up to 6) samples with different symbols in complexes barplots

einprot 0.4.3

  • Bugfix - use correct filter column names in TMT workflow

einprot 0.4.2

  • Allow filtering by (Sequest HT) score also for TMT workflow
  • Automatically generate QC pdf for TMT workflow
  • Make PCA plots interactive
  • Export volcano plots for significant complexes in TMT workflow
  • Add possibility to include interactive volcano plots in MQ workflow
  • Add direct links to PomBase and WormBase
  • Add link table to TMT workflow

einprot 0.4.1

  • Extract more information from the pdAnalysis file
  • Add possibility to include interactive volcano plots in TMT workflow
  • Add hierarchical clustering of samples to TMT workflow
  • Export all feature collection test results to text files
  • Subset all feature collections to features in the filtered data set (MQ + TMT)

einprot 0.4.0

  • Add PD-TMT workflow

einprot 0.3.6

  • Export text file with iBAQ values (+mean/sd) for all significant features (across comparisons)
  • Add table with direct links to UniProt pages for majority protein IDs

einprot 0.3.5

  • Update STRING to v11.5

einprot 0.3.4

  • Add function to list available complex DBs

einprot 0.3.3

  • Add STRING plots for each comparison
  • Shorten column labels in exported heatmap

einprot 0.3.2

  • Export centered heatmap to pdf
  • Add upset plot for significant proteins across comparisons
  • Add mergeGroups argument to create merged sample groups

einprot 0.3.1

  • Use semicolon instead of comma as separator for PMIDs in complex db
  • Include additional complex info in camera output also for t-test

einprot 0.3.0

  • Add more checks of input arguments to runMaxQuantAnalysis
  • Expand feature collections to include all variants found in the data set for a given gene
  • Internal improvements for increased robustness

einprot 0.2.2

  • Fix display of samples to include/exclude in summary table

einprot 0.2.1

  • Bugfix: fix parsing error for long lines

einprot 0.2.0

  • Collapse duplicates in complex db
  • Add path to complex db as argument to runMaxQuantAnalysis

einprot 0.1.1

  • Change path to submission list
  • Rotate axis labels in complex bar plots

einprot 0.1.0

  • Initial version